Genetic mechanisms of critical illness in Covid-19



Pairo-Castineira, Erola, Clohisey, Sara, Klaric, Lucija ORCID: 0000-0003-3105-8929, Bretherick, Andrew ORCID: 0000-0001-9258-3140, Rawlik, Konrad, Parkinson, Nick, Pasko, Dorota, Walker, Susan, Richmond, Anne, Fourman, Max Head ORCID: 0000-0001-7381-2278
et al (show 50 more authors) (2020) Genetic mechanisms of critical illness in Covid-19.

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Abstract

The subset of patients who develop critical illness in Covid-19 have extensive inflammation affecting the lungs 1 and are strikingly different from other patients: immunosuppressive therapy benefits critically-ill patients, but may harm some non-critical cases. 2 Since susceptibility to life-threatening infections and immune-mediated diseases are both strongly heritable traits, we reasoned that host genetic variation may identify mechanistic targets for therapeutic development in Covid-19. 3 GenOMICC (Genetics Of Mortality In Critical Care, genomicc.org ) is a global collaborative study to understand the genetic basis of critical illness. Here we report the results of a genome-wide association study (GWAS) in 2244 critically-ill Covid-19 patients from 208 UK intensive care units (ICUs), representing >95% of all ICU beds. Ancestry-matched controls were drawn from the UK Biobank population study and results were confirmed in GWAS comparisons with two other population control groups: the 100,000 genomes project and Generation Scotland. We identify and replicate three novel genome-wide significant associations, at chr19p13.3 (rs2109069, p = 3.98 × 10 −12 ), within the gene encoding dipeptidyl peptidase 9 ( DPP9 ), at chr12q24.13 (rs10735079, p =1.65 × 10 −8 ) in a gene cluster encoding antiviral restriction enzyme activators ( OAS1, OAS2, OAS3 ), and at chr21q22.1 (rs2236757, p = 4.99 × 10 −8 ) in the interferon receptor gene IFNAR2 . Consistent with our focus on extreme disease in younger patients with less comorbidity, we detect a stronger signal at the known 3p21.31 locus than previous studies (rs73064425, p = 4.77 × 10 −30 ). We identify potential targets for repurposing of licensed medications. Using Mendelian randomisation we found evidence in support of a causal link from low expression of IFNAR2 , and high expression of TYK2 , to life-threatening disease. Transcriptome-wide association in lung tissue revealed that high expression of the monocyte/macrophage chemotactic receptor CCR2 is associated with severe Covid-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms, and mediators of inflammatory organ damage in Covid-19. Both mechanisms may be amenable to targeted treatment with existing drugs. Large-scale randomised clinical trials will be essential before any change to clinical practice.

Item Type: Article
Uncontrolled Keywords: The GenOMICC Investigators, The ISARIC-4C Investigators, The Covid-19 Human Genetics Initiative
Depositing User: Symplectic Admin
Date Deposited: 12 Jan 2021 10:22
Last Modified: 02 Dec 2021 14:10
DOI: 10.1101/2020.09.24.20200048
Open Access URL: https://doi.org/10.1101/2020.09.24.20200048
URI: https://livrepository.liverpool.ac.uk/id/eprint/3112067